Mobility capillary electrophoresis–native mass spectrometry reveals the dynamic conformational equilibrium of calmodulin and its complexes

Zhao, Yi; Zhang, Wenjing; Hong, Jie; Yang, Lei; Wang, Yuanyuan; Qu, Feng; Xu, Wei

doi:10.1039/d4an00378k

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2024

DOI: 10.1039/d4an00378k

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Mobility capillary electrophoresis–native mass spectrometry reveals the dynamic conformational equilibrium of calmodulin and its complexes

Yi Zhao,

Wenjing Zhang,

Jie Hong

et al.

Abstract: Benefitting from the rapid evolution of artificial intelligence and structural biology, an expanding collection of high-resolution protein structures has greatly improved our understanding of protein functions. Yet, proteins are inherently...

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Cited by 1 publication

References 90 publications

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AI Assisted Native Proteomics: Delineating Ribosomal Protein Conformations Pre- and Post-Assembly

Zhang,

Sun,

et al. 2024

Preprint

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The simultaneous identification of proteins as well as their conformations in a biological system would greatly enhance our understanding of cellular mechanisms and disease. As an emerging technique, native proteomics analyzes proteins in their native states, facilitating the acquisition of protein stoichiometry, post-translational modifications (PTMs), and interactions with ligands. However, revealing protein conformations at the proteome scale remains a significant challenge. In this study, we propose an AI-assisted native proteomics method that integrates a protein structure prediction (PSP) module with top-down proteomics (TDP) and native mass spectrometry (nMS) to acquire both proteome identities and conformations. First, protein sequences and PTMs are obtained using the TDP method, while protein solvent-accessible surface area (SASA) is measured in parallel by nMS. These data are then input into the PSP module to acquire the most probable conformation of the protein under nMS experimental conditions. We validate the feasibility and accuracy of this method through the analysis of both a globular protein and an intrinsically disordered protein. Additionally, we apply this approach to delineate the conformations of ribosomal proteins pre- and post-assembly. Interactions of ribosomal proteins with drug molecules are also explored. By enabling proteome identification and conformation characterization from relatively small amounts of endogenous proteins, this method would bridge the gap between structural biology and conventional proteomics technologies.

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AI Assisted Native Proteomics: Delineating Ribosomal Protein Conformations Pre- and Post-Assembly

Zhang,

Sun,

et al. 2024

Preprint

View full text Add to dashboard Cite

show abstract

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Mobility capillary electrophoresis–native mass spectrometry reveals the dynamic conformational equilibrium of calmodulin and its complexes

Abstract: Benefitting from the rapid evolution of artificial intelligence and structural biology, an expanding collection of high-resolution protein structures has greatly improved our understanding of protein functions. Yet, proteins are inherently...

Cited by 1 publication

References 90 publications

AI Assisted Native Proteomics: Delineating Ribosomal Protein Conformations Pre- and Post-Assembly

AI Assisted Native Proteomics: Delineating Ribosomal Protein Conformations Pre- and Post-Assembly

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